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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ScreenR_1.13.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ScreenR.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ScreenR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ScreenR’ version ‘1.13.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ScreenR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) annotation_table.Rd:25: Lost braces
    25 |                  \url{https://cellecta.com/}{cellecta}}
       |                                             ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'compute_camera.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'select_number_barcode.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'unique_gene_symbols.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ScreenR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: find_zscore_hit
> ### Title: Title Find Z-score Hit
> ### Aliases: find_zscore_hit
> 
> ### ** Examples
> 
> object <- get0("object", envir = asNamespace("ScreenR"))
> table <- compute_metrics(object,
+     control = "TRT", treatment = "Time3",
+     day = "Time3"
+ )
> 
> # For the the median
> result <- find_zscore_hit(table, number_barcode = 6)
> head(result)
# A tibble: 6 × 2
  Gene     numberOfBarcode
  <chr>              <int>
1 Gene_102               8
2 Gene_115               7
3 Gene_117               7
4 Gene_124               7
5 Gene_129               7
6 Gene_13                7
> 
> # For the mean
> result <- find_zscore_hit(table, number_barcode = 6, metric = "mean")
Error in `dplyr::summarise()`:
ℹ In argument: `.data$numberOfBarcode`.
ℹ In group 1: `Gene = "Gene_1"`.
Caused by error:
! `.data$numberOfBarcode` must be size 1, not 3.
ℹ To return more or less than 1 row per group, use `reframe()`.
Backtrace:
     ▆
  1. ├─ScreenR::find_zscore_hit(table, number_barcode = 6, metric = "mean")
  2. │ └─... %>% ...
  3. ├─dplyr::filter(., .data$numberOfBarcode > number_barcode)
  4. ├─dplyr::summarise(., .data$numberOfBarcode)
  5. ├─dplyr:::summarise.grouped_df(., .data$numberOfBarcode)
  6. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
  7. │   └─base::withCallingHandlers(...)
  8. ├─dplyr:::dplyr_internal_error(...)
  9. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
 10. │   └─rlang:::signal_abort(cnd, .file)
 11. │     └─base::signalCondition(cnd)
 12. └─dplyr (local) `<fn>`(`<dpl:::__>`)
 13.   └─dplyr (local) handler(cnd)
 14.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
compute_metrics        15.471  1.543  17.017
find_robust_zscore_hit 12.123  0.420  12.544
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    5. ├─dplyr:::summarise.grouped_df(., .data$numberOfBarcode)
    6. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
    7. │   └─base::withCallingHandlers(...)
    8. ├─dplyr:::dplyr_internal_error(...)
    9. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
   10. │   └─rlang:::signal_abort(cnd, .file)
   11. │     └─base::signalCondition(cnd)
   12. └─dplyr (local) `<fn>`(`<dpl:::__>`)
   13.   └─dplyr (local) handler(cnd)
   14.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
  
  [ FAIL 5 | WARN 251 | SKIP 0 | PASS 59 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/ScreenR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ScreenR
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘ScreenR’ ...
** this is package ‘ScreenR’ version ‘1.13.1’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ScreenR)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(ScreenR)

Welcome to ScreenR
--------------------------

See ?ScreenR for a list of
available functions.

Enjoy!

> 
> test_check("ScreenR")
Saving _problems/test-MDS-52.R
Saving _problems/test-MDS-61.R
Saving _problems/test-MDS-70.R
Saving _problems/test-MDS-81.R
ScreenR count table containing:
 5320 rows
 15 columns
ScreenR annotation table containing:
 5320 rows
 5 columns
ScreenR normalized count table containing:
 5320 rows
 15 columns
ScreenR normalized data table containing:
 74480 rows
 9 columns
ScreenR annotation table containing:
 5320 rows
 5 columns
ScreenR annotation table containing:
 5320 rows
 5 columns
ScreenR count table containing:
 5320 rows
 15 columns
ScreenR count table containing:
 5320 rows
 15 columns
ScreenR normalized count table containing:
 5320 rows
 15 columns
ScreenR normalized count table containing:
 5320 rows
 15 columns
ScreenR normalized data table containing:
 74480 rows
 9 columns
ScreenR normalized data table containing:
 74480 rows
 9 columns
Saving _problems/test-statistics-105.R
Using classic mode.
[ FAIL 5 | WARN 251 | SKIP 0 | PASS 59 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-MDS.R:52:5'): plot_mds NULL ──────────────────────────────────
Expected `class(plot)[1]` to equal "gg".
Differences:
`actual`:   "ggplot2::ggplot"
`expected`: "gg"             

── Failure ('test-MDS.R:61:5'): plot_mds ───────────────────────────────────────
Expected `class(plot)[1]` to equal "gg".
Differences:
`actual`:   "ggplot2::ggplot"
`expected`: "gg"             

── Failure ('test-MDS.R:70:5'): plot_explained_variance ────────────────────────
Expected `class(plot)[[1]]` to equal "gg".
Differences:
`actual`:   "ggplot2::ggplot"
`expected`: "gg"             

── Failure ('test-MDS.R:81:5'): plot_explained_variance CUM ────────────────────
Expected `class(plot)[[1]]` to equal "gg".
Differences:
`actual`:   "ggplot2::ggplot"
`expected`: "gg"             

── Error ('test-statistics.R:105:5'): Find_Zscore_hit mean ─────────────────────
Error in `dplyr::summarise(., .data$numberOfBarcode)`: i In argument: `.data$numberOfBarcode`.
i In group 1: `Gene = "Gene_1"`.
Caused by error:
! `.data$numberOfBarcode` must be size 1, not 7.
i To return more or less than 1 row per group, use `reframe()`.
Backtrace:
     ▆
  1. ├─ScreenR::find_zscore_hit(table, number_barcode = 2, metric = "mean") at test-statistics.R:105:5
  2. │ └─... %>% ...
  3. ├─dplyr::filter(., .data$numberOfBarcode > number_barcode)
  4. ├─dplyr::summarise(., .data$numberOfBarcode)
  5. ├─dplyr:::summarise.grouped_df(., .data$numberOfBarcode)
  6. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
  7. │   └─base::withCallingHandlers(...)
  8. ├─dplyr:::dplyr_internal_error(...)
  9. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
 10. │   └─rlang:::signal_abort(cnd, .file)
 11. │     └─base::signalCondition(cnd)
 12. └─dplyr (local) `<fn>`(`<dpl:::__>`)
 13.   └─dplyr (local) handler(cnd)
 14.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)

[ FAIL 5 | WARN 251 | SKIP 0 | PASS 59 ]
Error:
! Test failures.
Execution halted